#include <LipidMemGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::LipidMemGrid:

[legend]

Public Member Functions
	LipidMemGrid ()
	default constructor More...

	~LipidMemGrid () override
	construct from LipidMemGrid input file LipidMemGrid(std::string const & filename); More...

GridBaseOP	clone () const override
	Make a copy of the grid, respecting the subclassing. More...

void	refresh (core::pose::Pose const &pose, core::Vector const &center, core::Size const &ligand_chain_id_to_exclude) override
	populate the grid with LipidMemGrid values in vector based on a passed pose More...

void	refresh (core::pose::Pose const &pose, core::Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude) override
	populate the grid with LipidMemGrid values in vector based on a passed pose More...

void	refresh (core::pose::Pose const &pose, core::Vector const &center) override
	populate the grids in the vector with Membrane ligand values based on a passed pose More...

core::Real	score (core::conformation::UltraLightResidue const &residue, core::Real const max_score, qsarMapCOP qsar_map) const override
	return the current score of an UltraLightResidue using the LipidMemGrid More...

core::Real	atom_score (core::conformation::UltraLightResidue const &residue, core::Size atomno, qsarMapCOP qsar_map) const override
	return the current score of an atom using the LipidMemGrid More...

core::Real	score (core::conformation::Residue const &residue, core::Real const max_score, qsarMapCOP qsar_map) const override
	return the current score of a residue using the LipidMemGrid More...

core::Real	atom_score (core::conformation::Residue const &residue, core::Size atomno, qsarMapCOP qsar_map) const override
	return the current score of an atom using the LipidMemGrid More...

utility::json_spirit::Value	serialize () const override
	Serialize the LipidMemGrid object into a json_spirit Value. More...

void	deserialize (utility::json_spirit::mObject data) override
	deserialize a json spirit Value into a LipidMemGrid object More...

void	parse_my_tag (utility::tag::TagCOP tag) override
	@setup a LipidMemGrid based on RosettaScripts input More...

void	show (std::ostream &out) const override
	Print a brief summary about this grid to the provided output stream. More...

std::string	hash_fingerprint () const override
	Return a string representing the settings which don't change based on reinitialization. More...

Public Member Functions inherited from protocols::qsar::scoring_grid::SingleGrid
	SingleGrid (std::string const &type)

	~SingleGrid () override

void	initialize (core::Vector const &center, core::Real width, core::Real resolution) override
	initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms). More...

void	set_chain (char chain) override
	set the chain around which to calculate the grid More...

char	get_chain ()
	get the chain around which the grid is calculated More...

utility::json_spirit::Value	serialize () const override
	serialize the SingleGrid to a json_spirit object More...

void	deserialize (utility::json_spirit::mObject data) override
	deserialize a json_spirit object to a SingleGrid More...

core::grid::CartGrid< core::Real > const &	get_grid () const
	return a constant reference to the grid More...

void	set_type (std::string type)
	set the grid type More...

std::string	get_type () const override
	return the grids type More...

void	set_center (core::Vector center)
	set the center of the grid More...

core::Vector	get_center () const
	get the center of the grid More...

core::Real	get_min_value () const
	get the max score value in the grid More...

core::Real	get_max_value () const
	get the minimum score value in the grid More...

core::Real	get_point (core::Real x, core::Real y, core::Real z) const
	get the value of a single point in the grid based on pdb coordinates More...

core::Real	get_point (core::Vector coords) const
	get the value of a single point in the grid based on pdb coordinates More...

numeric::xyzVector< core::Size >	get_dimensions ()
	get dimensions of the grid More...

core::Vector	get_pdb_coords (int x, int y, int z)
	get the pdb coordinates based on grid point coordinates More...

core::Vector	get_pdb_coords (core::grid::CartGrid< core::Real >::GridPt gridpt)
	get the pdb coordinates based on grid point coordinates More...

core::Real	score (core::conformation::UltraLightResidue const &residue, core::Real const max_score, qsarMapCOP qsar_map) const override
	return the current score of an UltraLightResidue using the current grid More...

core::Real	atom_score (core::conformation::UltraLightResidue const &residue, core::Size atomno, qsarMapCOP qsar_map) const override
	return the current score of an atom using the current grid More...

core::Real	score (core::conformation::Residue const &residue, core::Real const max_score, qsarMapCOP qsar_map) const override
	return the current score of a residue using the current grid More...

core::Real	atom_score (core::conformation::Residue const &residue, core::Size atomno, qsarMapCOP qsar_map) const override
	return the current score of an atom using the current grid More...

void	grid_to_kin (utility::io::ozstream &out, core::Real min_val, core::Real max_val, core::Size stride)

bool	is_in_grid (core::conformation::UltraLightResidue const &residue) const override
	check to see if residue is in grid More...

bool	is_in_grid (core::conformation::Residue const &residue) const override
	check to see if residue is in grid More...

std::list< std::pair< core::Vector, core::Real > >	get_point_value_list_within_range (core::Real lower_bound, core::Real upper_bound, core::Size stride) const

void	dump_BRIX (std::string const &prefix) const override
	output a BRIX formatted grid. This really does not work well but is being left for legacy purposes More...

void	set_sphere (core::Vector const &coords, core::Real radius, core::Real value)

void	set_ring (core::Vector const &coords, core::Real inner_radius, core::Real outer_radius, core::Real value)

void	diffuse_ring (core::Vector const &coords, core::Real radius, core::Real width, core::Real magnitude)

void	set_point (core::Vector const &coords, core::Real value)

void	set_distance_sphere_for_atom (core::Real const &atom_shell, core::Vector const &coords, core::Real cutoff)

void	set_score_sphere_for_atom (numeric::interpolation::spline::InterpolatorCOP lj_spline, core::Vector const &coords, core::Real cutoff)

void	fill_with_value (core::Real)
	@fill the entire grid with some value More...

void	show (std::ostream &out) const override
	Print a brief summary about this grid to the provided output stream. More...

Public Member Functions inherited from protocols::qsar::scoring_grid::GridBase
	GridBase ()

	~GridBase () override

Static Public Member Functions
static std::string	grid_name ()
	@bried Set Grid name More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Attributes
std::string	kbpot_file_

numeric::interpolation::spline::InterpolatorCOP	kbpot_spline_
	input lipid energies from database More...

std::string	lip_atom_
	interpolation More...

core::Real	mem_weight_
	lipid atom More...

Constructor & Destructor Documentation

◆ LipidMemGrid()

protocols::qsar::scoring_grid::LipidMemGrid::LipidMemGrid ( )

default constructor

Copy SingleGrid functions.

Referenced by clone().

◆ ~LipidMemGrid()

protocols::qsar::scoring_grid::LipidMemGrid::~LipidMemGrid ( )

override

construct from LipidMemGrid input file LipidMemGrid(std::string const & filename);

Destructor.

destructor

Member Function Documentation

◆ atom_score() [1/2]

core::Real protocols::qsar::scoring_grid::LipidMemGrid::atom_score	(	core::conformation::Residue const &	residue,
		core::Size	atomno,
		qsarMapCOP	qsar_map
	)		const

overridevirtual

return the current score of an atom using the LipidMemGrid

return the current score of an atom of the Residue using LipidMemGrid

Implements protocols::qsar::scoring_grid::GridBase.

References core::conformation::Residue::atom_name(), protocols::simple_filters::coords(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), lip_atom_, mem_weight_, score(), and core::conformation::Residue::xyz().

◆ atom_score() [2/2]

core::Real protocols::qsar::scoring_grid::LipidMemGrid::atom_score	(	core::conformation::UltraLightResidue const &	residue,
		core::Size	atomno,
		qsarMapCOP	qsar_map
	)		const

overridevirtual

return the current score of an atom using the LipidMemGrid

return the current score of an atom of the UltraLighResidue (ligand) using the LipidMemGrid

Implements protocols::qsar::scoring_grid::GridBase.

References protocols::simple_filters::coords(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), lip_atom_, mem_weight_, core::conformation::UltraLightResidue::residue(), and score().

◆ clone()

GridBaseOP protocols::qsar::scoring_grid::LipidMemGrid::clone ( ) const

overridevirtual

Make a copy of the grid, respecting the subclassing.

Make a copy of the grid, respecting the subclass.

Implements protocols::qsar::scoring_grid::SingleGrid.

References LipidMemGrid().

◆ deserialize()

void protocols::qsar::scoring_grid::LipidMemGrid::deserialize ( utility::json_spirit::mObject data )

overridevirtual

deserialize a json spirit Value into a LipidMemGrid object

Implements protocols::qsar::scoring_grid::GridBase.

References protocols::qsar::scoring_grid::SingleGrid::deserialize(), kbpot_spline_, lip_atom_, and mem_weight_.

◆ grid_name()

std::string protocols::qsar::scoring_grid::LipidMemGrid::grid_name ( )

static

@bried Set Grid name

Referenced by hash_fingerprint(), protocols::qsar::scoring_grid::LipidMemGridCreator::keyname(), and provide_xml_schema().

◆ hash_fingerprint()

std::string protocols::qsar::scoring_grid::LipidMemGrid::hash_fingerprint ( ) const

overridevirtual

Return a string representing the settings which don't change based on reinitialization.

Implements protocols::qsar::scoring_grid::SingleGrid.

References protocols::qsar::scoring_grid::SingleGrid::get_type(), grid_name(), kbpot_file_, kbpot_spline_, lip_atom_, and mem_weight_.

◆ parse_my_tag()

void protocols::qsar::scoring_grid::LipidMemGrid::parse_my_tag ( utility::tag::TagCOP tag )

overridevirtual

@setup a LipidMemGrid based on RosettaScripts input

Implements protocols::qsar::scoring_grid::SingleGrid.

References kbpot_file_, kbpot_spline_, lip_atom_, and mem_weight_.

◆ provide_xml_schema()

void protocols::qsar::scoring_grid::LipidMemGrid::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References grid_name(), and protocols::qsar::scoring_grid::xsd_type_definition_w_attributes().

Referenced by protocols::qsar::scoring_grid::LipidMemGridCreator::provide_xml_schema().

◆ refresh() [1/3]

void protocols::qsar::scoring_grid::LipidMemGrid::refresh	(	core::pose::Pose const &	pose,
		core::Vector const &	center
	)

overridevirtual

populate the grids in the vector with Membrane ligand values based on a passed pose

set grid and fill with lipid energies from spline

Implements protocols::qsar::scoring_grid::SingleGrid.

References protocols::membrane::compute_structure_based_embedding(), core::grid::CartGrid< T >::coords(), protocols::qsar::scoring_grid::SingleGrid::fill_with_value(), protocols::qsar::scoring_grid::SingleGrid::get_dimensions(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), kbpot_spline_, core::pose::Pose::membrane_info(), score(), protocols::qsar::scoring_grid::SingleGrid::set_point(), and protocols::qsar::scoring_grid::TR().

◆ refresh() [2/3]

void protocols::qsar::scoring_grid::LipidMemGrid::refresh	(	core::pose::Pose const &	pose,
		core::Vector const &	center,
		core::Size const &	ligand_chain_id_to_exclude
	)

overridevirtual

populate the grid with LipidMemGrid values in vector based on a passed pose

Implements protocols::qsar::scoring_grid::SingleGrid.

References core::conformation::membrane::center.

Referenced by refresh().

◆ refresh() [3/3]

void protocols::qsar::scoring_grid::LipidMemGrid::refresh	(	core::pose::Pose const &	pose,
		core::Vector const &	center,
		utility::vector1< core::Size >	ligand_chain_ids_to_exclude
	)

overridevirtual

populate the grid with LipidMemGrid values in vector based on a passed pose

Implements protocols::qsar::scoring_grid::SingleGrid.

References core::conformation::membrane::center, and refresh().

◆ score() [1/2]

core::Real protocols::qsar::scoring_grid::LipidMemGrid::score	(	core::conformation::Residue const &	residue,
		core::Real const	max_score,
		qsarMapCOP	qsar_map
	)		const

overridevirtual

return the current score of a residue using the LipidMemGrid

return the current score of a Residue using the LipidMemGrid

Implements protocols::qsar::scoring_grid::GridBase.

References core::conformation::Residue::atom_name(), protocols::simple_filters::coords(), protocols::qsar::scoring_grid::SingleGrid::get_grid(), protocols::qsar::scoring_grid::SingleGrid::get_point(), protocols::qsar::scoring_grid::SingleGrid::is_in_grid(), lip_atom_, mem_weight_, core::conformation::Residue::natoms(), score(), and core::conformation::Residue::xyz().

◆ score() [2/2]

core::Real protocols::qsar::scoring_grid::LipidMemGrid::score	(	core::conformation::UltraLightResidue const &	residue,
		core::Real const	max_score,
		qsarMapCOP	qsar_map
	)		const